November 2020 - ChimeraX-users - RBVI Mailing Lists

Command development
by Eric Pettersen 17 Nov '20

17 Nov '20

For any developers that will be implementing their own commands, we have put up a page about the considerations to think about when deciding on the command name and syntax, here: Command Style Guide — ChimeraX 1.2 documentation <https://www.cgl.ucsf.edu/chimerax/docs/devel/command_style.html> --Eric Eric Pettersen UCSF Computer Graphics Lab

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Atom specifier of manually selected group
by André Graça 17 Nov '20

17 Nov '20

Hi, I was wondering if there is any command that allows to list the atom specifiers for manually selected atoms using the ctrl drag and drop method. If there is one, I did not manage to frame my question properly to find it in the documentation, and I would appreciate some guidance. Thank you, André Graça

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Default movie image directory
by Daniel Asarnow 15 Nov '20

15 Nov '20

Hi, What is the default image directory when rendering on a movie on OS X? ChimeraX crashed while I was rendering (due to running out of space) and it seems like the images are taking up a lot of space somewhere. Thanks, -da

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[new-map-options] Error when using the "subregion" option
by Arthur Ecoffet 13 Nov '20

13 Nov '20

Dear ChimeraX developers, When using the "subregion" option for different map-related functions (volume morph, volume copy) I encountered the following error : *ValueError: could not broadcast input array from shape (150,150,150) into shape (151,151,151)File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\map\volume.py", line 982, in writable_copy*g.array*[:,:,:] = self.region_matrix(r) *If you want to reproduce the error, I worked on EMDB22000 and I typed in the console : *volume copy #1 subregion 150,150,150,300,300,300 *alternatively *volume morph #1 #2 subregion 150,150,150,300,300,300 * raises the same error. I tried on two versions of ChimeraX (including the last stable from September) and got the same error twice. Would you have any idea how to solve this? Thanks very much, Best, Arthur

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ChimeraX
by Reed, Scott 13 Nov '20

13 Nov '20

Helo, I am interested in getting a copy of the ChimeraX GitHub repository. I have some python code running on chimera that I would like to update to ChimeraX. Thanks, Scott Scott Reed scott.reed(a)ucdenver.edu<mailto:scott.reed@ucdenver.edu> https://ucdenver.zoom.us/j/3152346473

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Selecting a webcam
by Lewandowski, Jozef 13 Nov '20

13 Nov '20

Hi, If I have multiple webcams installed on my laptop how would I select a specific webcam to use with the webcam command? Thanks, Józef

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Clipping Map | Slices in Plane Flattening to white
by Anderson, Jacob 13 Nov '20

13 Nov '20

Dear ChimeraX Developers and Users, When I slice a colored map (not model), the portion of the map cut by the plane are flattened to white. Is there a way to make the section cut by the plane the same color as the map at that location? I include an example here. Ideally, we would like for these white areas to be the orange color of the map here. And in the bottom right, pink. [cid:21ec6d86-961b-4d86-81c4-c183a5da3447] ~jacob

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change color for map slices
by Gui, Miao 13 Nov '20

13 Nov '20

Dear chimeraX team, I have some issues when coloring a cryo-EM map. I firstly colored a map gray, then fitted the models in the map and colored the map by zone. I'd like to generate a cross-section slice, but the slice color is always white. Please see the attached image for example, the green surface color is good, but the slice is white. Is there a feature I could use to cap the slices with colors? Thanks. Best wishes, Miao

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Re: [chimerax-users] Help please on how to create a homodimer with different chain IDs using sym command
by Elaine Meng 10 Nov '20

10 Nov '20

Dear Scott, That's great! We like to hear that ChimeraX is used in teaching. To get the dimer, I guess you used open 2zhg sym #1 assembly 1 (since "sym #1" merely reports the assemblies available and does not add the other half). Then, the first half is model #1 containing chains A,B and the second half is model #2 also containing chains A,B. You can see you have two models in the "Models" panel on the right. Thus you can refer to the two A chains separately in the command line as #1/A and #2/A, or the entire models as #1 and #2. Command-line specification: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html> An alternative is to fetch the biounit directly, e.g. open 2zhg from pdbe_bio maxassemblies 1 In that case the DNA chains are A and AA and the protein ones are B and BA. You can see this information in the Log when the file is opened. For explanation of fetching and its options: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#fetch> Unless including private data, it's better to send questions to chimerax-users(a)cgl.ucsf.edu (CC'd here) rather than to me personally... then others may benefit, and the messages are kept in a searchable archive. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Nov 10, 2020, at 9:43 AM, Scott White <S.A.WHITE(a)bham.ac.uk> wrote: > > Dear Elaine, > > I am using ChimeraX for teaching. I want to be able to instruct how to create a homodimer, but to manipulate the separate chains, eg colour them differently. > > example: > open 2zhg (asu, one half of a homodimer) > sym #1 (create the other half) > > but both polypeptide chains are labelled Chain A. If I select "sel \a" I get the whole model. If I use right-mouse-button select by clicking, I get the atom in both chains selected. > > How can I manipulate the two polypeptide chains independently? I've tried playing with the various sym options, but I can't get that to work. I have tried using "split" command, but that splits the polypeptide and DNA chains into separate submodels, as expected. It won't split the two chains A into a A and C, for example. > > Any guidance please? > > I know I could save the file and use a file editor such as vi, but this is a class for students and I was hoping to do it all by ChimeraX. > > I'm working with ChimeraX version 1.0 > > thanks for your help, > Scott

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Re: [chimerax-users] Assistance: ChimeraX save scene
by Guillaume Gaullier 10 Nov '20

10 Nov '20

Priyanka, Sorry, but I don’t know the answer to your question off the top of my head, and I won’t have time to figure it out this week. As I already recommended, please email the list chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> (copied to this email) and not me (or anybody else) individually: you will get answers faster this way, because the people who develop ChimeraX monitor this mailing-list and are really good at answering questions; it is also more useful for everybody, since questions and answers sent to the list get archived and become searchable on the list’s website. I hope somebody can help you solve your problem soon. Good luck. Guillaume > On 10 Nov 2020, at 04:36, Priyanka Abeyrathne <pabeyrat(a)gmail.com> wrote: > > Hi Guillaume, > > I used the "view name myview" and "view myview" to save the scene in ChimeraX. It worked only one time as scene saved as ---.cxs file. I tried the scene command again but it didn't work. Any suggestions? > > Thanks a lot. > Priyanka > > On Mon, Oct 12, 2020 at 3:41 AM Guillaume Gaullier <guillaume(a)gaullier.org <mailto:guillaume@gaullier.org>> wrote: > Hi Priyanka, > > If what you need is a command that can restore the camera’s position to a previously saved state after you moved it, then this should be helpful: > > 1. set the scene the way you want it > 2. run command "view name myview" ("myview" can be any name); what this does is assign a name to the current view (camera settings) > 3. rotate or translate, move around, etc. > 4. run command "view myview", which should reset the camera settings to what they were when you did step 2 above > > I believe named views are saved with the session, so you should be able to use them even after you save and close, then reopen your .cxs file. > > You will find more details in the documentation, with command "help view". Also here: https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name> > > I hope this helps, > > Guillaume > > >> On 11 Oct 2020, at 22:10, Priyanka Abeyrathne <pabeyrat(a)gmail.com <mailto:pabeyrat@gmail.com>> wrote: >> >> Hi All, >> >> Is there a save scene command in ChimeraX? >> >> Thanks, >> Priyanka >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> >

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